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java.lang.Objectorg.jmol.api.JmolSimpleViewer
org.jmol.api.JmolViewer
public abstract class JmolViewer
This is the high-level API for the JmolViewer for simple access.
We will implement a low-level API at some point
Field Summary | |
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java.lang.String |
menuStructure
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Constructor Summary | |
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JmolViewer()
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Method Summary | |
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abstract void |
addSelectionListener(JmolSelectionListener listener)
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static JmolViewer |
allocateViewer(java.awt.Component awtComponent,
JmolAdapter jmolAdapter)
OK, but safer to assign htmlName, URL bases, comandOptions, and statusListener now. |
static JmolViewer |
allocateViewer(java.awt.Component awtComponent,
JmolAdapter jmolAdapter,
java.lang.String htmlName,
java.net.URL documentBase,
java.net.URL codeBase,
java.lang.String commandOptions,
JmolStatusListener statusListener)
This is the main access point for creating an application or applet viewer. |
abstract boolean |
checkHalt(java.lang.String strCommand,
boolean isInterrupt)
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static boolean |
checkOption(JmolViewer viewer,
java.lang.String option)
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abstract boolean |
checkPrivateKey(double privateKey)
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abstract void |
clearMeasurements()
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abstract void |
clearSelection()
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abstract java.lang.String |
clipImage(java.lang.String text)
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abstract java.lang.Object |
createImage(java.lang.String fileName,
java.lang.String type,
java.lang.Object text_or_bytes,
int quality,
int width,
int height)
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abstract void |
deleteMeasurement(int i)
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abstract java.lang.String |
evalStringQuiet(java.lang.String script)
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abstract int |
findNearestAtomIndex(int x,
int y)
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abstract java.lang.String |
generateOutput(java.lang.String type,
java.lang.String[] fileName,
int width,
int height)
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abstract java.lang.String |
getAltLocListInModel(int modelIndex)
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abstract int |
getAnimationFps()
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abstract int |
getAtomArgb(int atomIndex)
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abstract int |
getAtomCount()
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abstract int |
getAtomCountInModel(int modelIndex)
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abstract java.lang.String |
getAtomInfo(int atomIndex)
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abstract int |
getAtomModelIndex(int atomIndex)
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abstract java.lang.String |
getAtomName(int atomIndex)
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abstract int |
getAtomNumber(int atomIndex)
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abstract javax.vecmath.Point3f |
getAtomPoint3f(int atomIndex)
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abstract float |
getAtomRadius(int atomIndex)
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abstract boolean |
getAutoBond()
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abstract boolean |
getAxesOrientationRasmol()
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abstract int |
getBackgroundArgb()
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abstract int |
getBondArgb1(int bondIndex)
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abstract int |
getBondArgb2(int bondIndex)
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abstract int |
getBondCount()
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abstract int |
getBondCountInModel(int modelIndex)
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abstract int |
getBondModelIndex(int bondIndex)
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abstract int |
getBondOrder(int bondIndex)
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abstract javax.vecmath.Point3f |
getBondPoint3f1(int bondIndex)
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abstract javax.vecmath.Point3f |
getBondPoint3f2(int bondIndex)
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abstract float |
getBondRadius(int bondIndex)
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abstract float |
getBondTolerance()
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abstract boolean |
getBooleanProperty(java.lang.String propertyName)
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boolean |
getBooleanProperty(java.lang.String key,
boolean doICare)
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abstract int |
getChainCount()
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abstract int |
getChainCountInModel(int modelIindex)
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abstract java.lang.String |
getData(java.lang.String atomExpression,
java.lang.String type)
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abstract java.awt.Component |
getDisplay()
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abstract int |
getDisplayModelIndex()
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abstract java.util.BitSet |
getElementsPresentBitSet(int modelIndex)
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abstract java.lang.String |
getErrorMessage()
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abstract java.lang.String |
getErrorMessageUntranslated()
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abstract java.lang.Object |
getFileAsBytes(java.lang.String fullPathName,
java.io.OutputStream os)
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abstract java.lang.String |
getFileAsString(java.lang.String filename)
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abstract boolean |
getFileAsString(java.lang.String[] data,
int nBytesMax,
boolean doSpecialLoad)
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abstract int |
getGroupCount()
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abstract int |
getGroupCountInModel(int modelIndex)
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abstract java.util.Hashtable |
getHeteroList(int modelIndex)
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abstract java.lang.Object |
getImageAs(java.lang.String type,
int quality,
int width,
int height,
java.lang.String fileName,
java.io.OutputStream os)
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abstract java.lang.String |
getJavaVendor()
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abstract java.lang.String |
getJavaVersion()
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static java.lang.String |
getJmolVersion()
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abstract short |
getMadBond()
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abstract int |
getMeasurementCount()
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abstract int[] |
getMeasurementCountPlusIndices(int i)
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abstract java.lang.String |
getMeasurementStringValue(int i)
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abstract float |
getMinBondDistance()
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abstract JmolAdapter |
getModelAdapter()
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abstract java.util.Hashtable |
getModelAuxiliaryInfo(int modelIndex)
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abstract java.lang.Object |
getModelAuxiliaryInfo(int modelIndex,
java.lang.String keyName)
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abstract int |
getModelCount()
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abstract java.lang.String |
getModelFileName(int modelIndex)
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abstract java.lang.String |
getModelName(int modelIndex)
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abstract int |
getModelNumber(int modelIndex)
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abstract java.lang.String |
getModelNumberDotted(int modelIndex)
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abstract java.util.Properties |
getModelProperties(int modelIndex)
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abstract java.lang.String |
getModelProperty(int modelIndex,
java.lang.String propertyName)
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abstract java.util.Hashtable |
getModelSetAuxiliaryInfo()
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abstract java.lang.String |
getModelSetFileName()
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abstract java.lang.String |
getModelSetName()
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abstract java.lang.String |
getModelSetPathName()
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abstract java.util.Properties |
getModelSetProperties()
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abstract int |
getMotionEventNumber()
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abstract java.lang.String |
getOperatingSystemName()
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abstract java.lang.Object |
getParameter(java.lang.String name)
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abstract int |
getPercentVdwAtom()
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abstract boolean |
getPerspectiveDepth()
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abstract int |
getPolymerCount()
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abstract int |
getPolymerCountInModel(int modelIndex)
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abstract javax.vecmath.Point3f[] |
getPolymerLeadMidPoints(int modelIndex,
int polymerIndex)
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abstract float |
getRotationRadius()
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abstract int |
getScreenHeight()
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java.awt.Image |
getScreenImage()
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abstract java.awt.Image |
getScreenImage(java.awt.Graphics g)
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abstract int |
getScreenWidth()
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abstract int |
getSelectionCount()
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abstract java.lang.String |
getSetHistory(int howFarBack)
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abstract boolean |
getShowAxes()
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abstract boolean |
getShowBbcage()
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abstract boolean |
getShowHydrogens()
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abstract boolean |
getShowMeasurements()
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abstract java.util.BitSet |
getSmartsMatch(java.lang.String smarts,
java.util.BitSet bsSelected)
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abstract java.lang.String |
getStateInfo()
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abstract javax.vecmath.Matrix4f |
getUnscaledTransformMatrix()
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abstract java.util.BitSet |
getVisibleFramesBitSet()
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abstract int |
getZoomPercent()
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abstract float |
getZoomPercentFloat()
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abstract void |
haltScriptExecution()
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abstract boolean |
handleOldJvm10Event(java.awt.Event e)
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abstract boolean |
haveFrame()
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abstract boolean |
havePartialCharges()
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abstract void |
homePosition()
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abstract boolean |
isApplet()
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abstract boolean |
isScriptExecuting()
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abstract java.lang.String |
loadInline(java.util.List arrayData,
boolean isAppend)
NOTE: THIS METHOD DOES NOT PRESERVE THE STATE |
abstract java.lang.String |
loadInline(java.lang.String strModel)
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abstract java.lang.String |
loadInline(java.lang.String[] arrayModels)
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abstract java.lang.String |
loadInline(java.lang.String[] arrayModels,
boolean isAppend)
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abstract java.lang.String |
loadInline(java.lang.String strModel,
boolean isAppend)
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abstract java.lang.String |
loadInline(java.lang.String strModel,
char newLine)
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abstract boolean |
modelHasVibrationVectors(int modelIndex)
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abstract void |
notifyViewerRepaintDone()
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abstract void |
openFileAsynchronously(java.lang.String fileName)
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abstract java.lang.String |
openReader(java.lang.String fullPathName,
java.lang.String fileName,
java.io.Reader reader)
Opens the file and creates the model set, given the reader. |
abstract void |
popHoldRepaint()
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abstract void |
pushHoldRepaint()
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abstract void |
rebond()
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abstract void |
refresh(int isOrientationChange,
java.lang.String strWhy)
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abstract void |
releaseScreenImage()
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abstract void |
removeSelectionListener(JmolSelectionListener listener)
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abstract void |
renderScreenImage(java.awt.Graphics gLeft,
java.awt.Graphics gRight,
java.awt.Dimension size,
java.awt.Rectangle clip)
an added class for rendering stereo in two independent applets |
abstract void |
rotateFront()
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abstract void |
rotateX(float radians)
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abstract void |
rotateX(int degrees)
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abstract void |
rotateY(float radians)
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abstract void |
rotateY(int degrees)
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abstract void |
rotateZ(float radians)
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abstract java.lang.String |
script(java.lang.String script)
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abstract java.lang.Object |
scriptCheck(java.lang.String script)
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abstract java.lang.String |
scriptWait(java.lang.String script)
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abstract java.lang.Object |
scriptWaitStatus(java.lang.String script,
java.lang.String statusList)
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abstract void |
selectAll()
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abstract void |
setAnimationFps(int framesPerSecond)
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abstract void |
setAppletContext(java.lang.String htmlName,
java.net.URL documentBase,
java.net.URL codeBase,
java.lang.String commandOptions)
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abstract void |
setAutoBond(boolean autoBond)
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abstract void |
setAxesOrientationRasmol(boolean axesMessedUp)
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abstract void |
setBondTolerance(float bondTolerance)
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abstract void |
setBooleanProperty(java.lang.String propertyName,
boolean value)
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abstract void |
setCenterSelected()
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abstract void |
setColorBackground(java.lang.String colorName)
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abstract void |
setDebugScript(boolean debugScript)
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abstract void |
setFloatProperty(java.lang.String propertyName,
float value)
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abstract void |
setFrankOn(boolean frankOn)
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abstract void |
setIntProperty(java.lang.String propertyName,
int value)
|
abstract void |
setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
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abstract void |
setJmolDefaults()
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abstract void |
setJmolStatusListener(JmolStatusListener jmolStatusListener)
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abstract void |
setMarBond(short marBond)
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abstract void |
setMinBondDistance(float minBondDistance)
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abstract void |
setModeMouse(int modeMouse)
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abstract void |
setPercentVdwAtom(int percentVdwAtom)
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abstract void |
setPerspectiveDepth(boolean perspectiveDepth)
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abstract void |
setRasmolDefaults()
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abstract void |
setScreenDimension(java.awt.Dimension dim)
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abstract void |
setSelectionHalos(boolean haloEnabled)
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abstract void |
setSelectionSet(java.util.BitSet newSelection)
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abstract void |
setShowAxes(boolean showAxes)
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abstract void |
setShowBbcage(boolean showBbcage)
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abstract void |
setShowHydrogens(boolean showHydrogens)
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abstract void |
setShowMeasurements(boolean showMeasurements)
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abstract void |
setStringProperty(java.lang.String propertyName,
java.lang.String value)
|
abstract void |
setVectorScale(float vectorScaleValue)
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abstract void |
setVibrationPeriod(float vibrationPeriod)
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abstract void |
setVibrationScale(float vibrationScaleValue)
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abstract boolean |
showModelSetDownload()
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abstract void |
showUrl(java.lang.String urlString)
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abstract void |
syncScript(java.lang.String script,
java.lang.String applet)
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abstract void |
writeTextFile(java.lang.String string,
java.lang.String data)
|
Methods inherited from class org.jmol.api.JmolSimpleViewer |
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allocateSimpleViewer, evalFile, evalString, getProperty, openDOM, openFile, openFiles, openStringInline, renderScreenImage |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public java.lang.String menuStructure
Constructor Detail |
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public JmolViewer()
Method Detail |
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public static JmolViewer allocateViewer(java.awt.Component awtComponent, JmolAdapter jmolAdapter, java.lang.String htmlName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions, JmolStatusListener statusListener)
awtComponent
- jmolAdapter
- htmlName
- documentBase
- codeBase
- commandOptions
- statusListener
-
public abstract java.util.BitSet getSmartsMatch(java.lang.String smarts, java.util.BitSet bsSelected)
public abstract void renderScreenImage(java.awt.Graphics gLeft, java.awt.Graphics gRight, java.awt.Dimension size, java.awt.Rectangle clip)
gLeft
- gRight
- size
- clip
- public static JmolViewer allocateViewer(java.awt.Component awtComponent, JmolAdapter jmolAdapter)
awtComponent
- jmolAdapter
-
public static java.lang.String getJmolVersion()
public static boolean checkOption(JmolViewer viewer, java.lang.String option)
public abstract java.lang.String generateOutput(java.lang.String type, java.lang.String[] fileName, int width, int height)
public abstract void setJmolCallbackListener(JmolCallbackListener jmolCallbackListener)
public abstract void setJmolStatusListener(JmolStatusListener jmolStatusListener)
public abstract void setAppletContext(java.lang.String htmlName, java.net.URL documentBase, java.net.URL codeBase, java.lang.String commandOptions)
public abstract boolean checkHalt(java.lang.String strCommand, boolean isInterrupt)
public abstract void haltScriptExecution()
public abstract java.lang.String getOperatingSystemName()
public abstract java.lang.String getJavaVersion()
public abstract java.lang.String getJavaVendor()
public abstract boolean haveFrame()
public abstract void pushHoldRepaint()
public abstract void popHoldRepaint()
public abstract java.lang.String getData(java.lang.String atomExpression, java.lang.String type)
public abstract void setScreenDimension(java.awt.Dimension dim)
public abstract int getScreenWidth()
public abstract int getScreenHeight()
public java.awt.Image getScreenImage()
public abstract java.awt.Image getScreenImage(java.awt.Graphics g)
public abstract void releaseScreenImage()
public abstract void writeTextFile(java.lang.String string, java.lang.String data)
public abstract java.lang.String clipImage(java.lang.String text)
text
- null here clips image; String clips text
public abstract java.lang.Object createImage(java.lang.String fileName, java.lang.String type, java.lang.Object text_or_bytes, int quality, int width, int height)
fileName
- type
- text_or_bytes
- quality
- width
- height
-
public abstract java.lang.Object getImageAs(java.lang.String type, int quality, int width, int height, java.lang.String fileName, java.io.OutputStream os)
type
- "PNG", "JPG", "JPEG", "JPG64", "PPM", "GIF"quality
- width
- height
- fileName
- os
-
public abstract boolean handleOldJvm10Event(java.awt.Event e)
public abstract int getMotionEventNumber()
public abstract java.lang.String openReader(java.lang.String fullPathName, java.lang.String fileName, java.io.Reader reader)
fullPathName
- fileName
- reader
-
public abstract void showUrl(java.lang.String urlString)
public abstract int getMeasurementCount()
public abstract java.lang.String getMeasurementStringValue(int i)
public abstract int[] getMeasurementCountPlusIndices(int i)
public abstract java.awt.Component getDisplay()
public abstract java.util.BitSet getElementsPresentBitSet(int modelIndex)
public abstract int getAnimationFps()
public abstract int findNearestAtomIndex(int x, int y)
public abstract java.lang.String script(java.lang.String script)
public abstract java.lang.Object scriptCheck(java.lang.String script)
public abstract java.lang.String scriptWait(java.lang.String script)
public abstract java.lang.Object scriptWaitStatus(java.lang.String script, java.lang.String statusList)
public abstract java.lang.String loadInline(java.lang.String strModel)
public abstract java.lang.String loadInline(java.lang.String strModel, boolean isAppend)
public abstract java.lang.String loadInline(java.lang.String strModel, char newLine)
public abstract java.lang.String loadInline(java.lang.String[] arrayModels)
public abstract java.lang.String loadInline(java.lang.String[] arrayModels, boolean isAppend)
arrayModels
- and array of models, each of which is a StringisAppend
-
public abstract java.lang.String loadInline(java.util.List arrayData, boolean isAppend)
arrayData
- a List of models, where each model is either a String
or a String[] or a VectorisAppend
- TRUE to append models (no ZAP)
public abstract java.lang.String evalStringQuiet(java.lang.String script)
public abstract boolean isScriptExecuting()
public abstract java.lang.String getModelSetName()
public abstract java.lang.String getModelSetFileName()
public abstract java.lang.String getModelSetPathName()
public abstract java.lang.String getFileAsString(java.lang.String filename)
public abstract boolean getFileAsString(java.lang.String[] data, int nBytesMax, boolean doSpecialLoad)
public abstract java.util.Properties getModelSetProperties()
public abstract java.util.Hashtable getModelSetAuxiliaryInfo()
public abstract int getModelNumber(int modelIndex)
public abstract java.lang.String getModelName(int modelIndex)
public abstract java.lang.String getModelNumberDotted(int modelIndex)
public abstract java.util.Properties getModelProperties(int modelIndex)
public abstract java.lang.String getModelProperty(int modelIndex, java.lang.String propertyName)
public abstract java.util.Hashtable getModelAuxiliaryInfo(int modelIndex)
public abstract java.lang.Object getModelAuxiliaryInfo(int modelIndex, java.lang.String keyName)
public abstract boolean modelHasVibrationVectors(int modelIndex)
public abstract int getModelCount()
public abstract int getDisplayModelIndex()
public abstract java.util.BitSet getVisibleFramesBitSet()
public abstract int getAtomCount()
public abstract int getBondCount()
public abstract int getGroupCount()
public abstract int getChainCount()
public abstract int getPolymerCount()
public abstract int getAtomCountInModel(int modelIndex)
public abstract int getBondCountInModel(int modelIndex)
public abstract int getGroupCountInModel(int modelIndex)
public abstract int getChainCountInModel(int modelIindex)
public abstract int getPolymerCountInModel(int modelIndex)
public abstract int getSelectionCount()
public abstract void addSelectionListener(JmolSelectionListener listener)
public abstract void removeSelectionListener(JmolSelectionListener listener)
public abstract void homePosition()
public abstract java.util.Hashtable getHeteroList(int modelIndex)
public abstract boolean getPerspectiveDepth()
public abstract boolean getShowHydrogens()
public abstract boolean getShowMeasurements()
public abstract boolean getShowAxes()
public abstract boolean getShowBbcage()
public abstract int getAtomNumber(int atomIndex)
public abstract java.lang.String getAtomName(int atomIndex)
public abstract java.lang.String getAtomInfo(int atomIndex)
public abstract float getRotationRadius()
public abstract int getZoomPercent()
public abstract float getZoomPercentFloat()
public abstract javax.vecmath.Matrix4f getUnscaledTransformMatrix()
public abstract int getBackgroundArgb()
public abstract float getAtomRadius(int atomIndex)
public abstract javax.vecmath.Point3f getAtomPoint3f(int atomIndex)
public abstract int getAtomArgb(int atomIndex)
public abstract int getAtomModelIndex(int atomIndex)
public abstract float getBondRadius(int bondIndex)
public abstract javax.vecmath.Point3f getBondPoint3f1(int bondIndex)
public abstract javax.vecmath.Point3f getBondPoint3f2(int bondIndex)
public abstract int getBondArgb1(int bondIndex)
public abstract int getBondArgb2(int bondIndex)
public abstract int getBondOrder(int bondIndex)
public abstract int getBondModelIndex(int bondIndex)
public abstract javax.vecmath.Point3f[] getPolymerLeadMidPoints(int modelIndex, int polymerIndex)
public abstract boolean getAxesOrientationRasmol()
public abstract int getPercentVdwAtom()
public abstract boolean getAutoBond()
public abstract short getMadBond()
public abstract float getBondTolerance()
public abstract void rebond()
public abstract float getMinBondDistance()
public abstract void refresh(int isOrientationChange, java.lang.String strWhy)
public abstract boolean showModelSetDownload()
public abstract void notifyViewerRepaintDone()
public abstract boolean getBooleanProperty(java.lang.String propertyName)
public boolean getBooleanProperty(java.lang.String key, boolean doICare)
public abstract java.lang.Object getParameter(java.lang.String name)
public abstract java.lang.String getSetHistory(int howFarBack)
public abstract boolean havePartialCharges()
public abstract boolean isApplet()
public abstract java.lang.String getAltLocListInModel(int modelIndex)
public abstract java.lang.String getStateInfo()
public abstract void syncScript(java.lang.String script, java.lang.String applet)
public abstract void setColorBackground(java.lang.String colorName)
public abstract void setShowAxes(boolean showAxes)
public abstract void setShowBbcage(boolean showBbcage)
public abstract void setJmolDefaults()
public abstract void setRasmolDefaults()
public abstract void setBooleanProperty(java.lang.String propertyName, boolean value)
public abstract void setIntProperty(java.lang.String propertyName, int value)
public abstract void setFloatProperty(java.lang.String propertyName, float value)
public abstract void setStringProperty(java.lang.String propertyName, java.lang.String value)
public abstract void setModeMouse(int modeMouse)
public abstract void setShowHydrogens(boolean showHydrogens)
public abstract void setShowMeasurements(boolean showMeasurements)
public abstract void setPerspectiveDepth(boolean perspectiveDepth)
public abstract void setAutoBond(boolean autoBond)
public abstract void setMarBond(short marBond)
public abstract void setBondTolerance(float bondTolerance)
public abstract void setMinBondDistance(float minBondDistance)
public abstract void setAxesOrientationRasmol(boolean axesMessedUp)
public abstract void setPercentVdwAtom(int percentVdwAtom)
public abstract void setAnimationFps(int framesPerSecond)
public abstract void setFrankOn(boolean frankOn)
public abstract void setDebugScript(boolean debugScript)
public abstract void deleteMeasurement(int i)
public abstract void clearMeasurements()
public abstract void setVectorScale(float vectorScaleValue)
public abstract void setVibrationScale(float vibrationScaleValue)
public abstract void setVibrationPeriod(float vibrationPeriod)
public abstract void selectAll()
public abstract void clearSelection()
public abstract void setSelectionSet(java.util.BitSet newSelection)
public abstract void setSelectionHalos(boolean haloEnabled)
public abstract void setCenterSelected()
public abstract void rotateFront()
public abstract void rotateX(int degrees)
public abstract void rotateY(int degrees)
public abstract void rotateX(float radians)
public abstract void rotateY(float radians)
public abstract void rotateZ(float radians)
public abstract JmolAdapter getModelAdapter()
public abstract void openFileAsynchronously(java.lang.String fileName)
public abstract java.lang.Object getFileAsBytes(java.lang.String fullPathName, java.io.OutputStream os)
public abstract java.lang.String getErrorMessage()
public abstract java.lang.String getErrorMessageUntranslated()
public abstract java.lang.String getModelFileName(int modelIndex)
public abstract boolean checkPrivateKey(double privateKey)
|
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PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |